Computational protocol: Double-stranded RNA analog and type I interferon regulate expression of Trem paired receptors in murine myeloid cells

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Protocol publication

[…] A BLAST search of the vertebrate Trem genes was performed by the amino acid sequences of human and mouse Trem genes as queries using the Ensembl genome databases (http://www.ensembl.org/index.html). The genome assembly versions of species used in this paper were as follows: GRCh37 of human, GRCm38 of mouse, OryCun2.0 of Rabbit, CanFam3.1 of Dog, EquCab2 of Horse, UMD3.1 of Cow, Sscrofa10.2 of Pig, BROADO5 of opossum, Galgal4 of chicken, JGI_4.2 of frog and Zv9 of zebrafish. Domain structures of Trem proteins were analyzed by SMART program (http://smart.embl-heidelberg.de). A phylogenetic tree based on the amino acid sequences of Ig domain was constructed by the Neighbor-joining (NJ) method in the ClustalX version 2 program and the MEGA version 5 program [, ]. The distance matrix was obtained by calculating p-distances for all pairs of sequences. Sites containing gaps were excluded from the analysis using the pairwise deletion option. The reliability of branching patterns was assessed by bootstrap analysis (1000 replications). Vertebrate Trem genes used for phylogenetic and comparative genomic analysis are listed in supplementary Table . […]

Pipeline specifications

Software tools Clustal W, MEGA
Application Phylogenetics
Organisms Mus musculus
Chemicals Poly I-C, Tyrosine